Last year (or so) I also suggested that the Runway Select box auto-close after selecting a Runway.
Most users didn't like that, and the sense I got then was that iFly tried not to do too many automatic thigns with the UI.
Perhaps now that you've brought it up again, they will revisit it. The only downside I can see to autoclose is when I fatfinger the wrong runway. Then I would have to go thru the entire process again. But since that's not supposed to happen much ...
Another thought I had was that, for those who want it as an option, if there were an optional AutoZoom, then perhaps a query box could popup with that, asking the user what runway they want selected? (I don't like AutoZoom, so this won't work for me.)
And one more idea - in the Airport page, which, presumably, most of us will be checking about a half hour away from landing, and which also has runway info on it, perhaps there could be check boxes next to each runway for users to "pre-select" which runway to extend? (Although we might be in range for the ATIS/AWOS yet.)
As for iFly knowing which runway is a calm wind runway - since that's a text based thing, and since it's often a local preference, there might not be an easy way to automatically gather that info. And it might be that iFly doesn't want that liability? (At best, perhaps a note (Calm) next to a runway in the Selector box where someone has hand coded which is a preferred runway?)